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Como elemento genético altamente conservado, el polen es fundamental en el reconocimiento de un taxón. Por tanto, se estudió la diversidad de algunas especies de Passiflora L., por medio de caracterización palinológica, mostrando su importancia como herramienta para elucidar la controversia taxonómica del género. Para esto se tomaron 30 muestras de polen, las cuales fueron analizadas bajo microscopías óptica (acetólisis) y electrónica de barrido MEB, representando 20 especies de Passiflora. Se incluyó la especie-tipo del género, P. incarnata, y P. macrophylla (única especie arborescente monopodial del subgénero Astrophea). Palabras-clave: género Passiflora, polen, acetólisis, MEB

In this twin study we show that the penchant for a particular sector of employment has a genetic element: monozygotic twins evidencing a greater similarity of sector choice than dizygotic twins. Th...

There is a critical need for further research into methods to control biological populations. Numerous challenges to agriculture, ecological systems, and human health could be mitigated by the targeted reduction and management of key species (e.g. pests, parasites, and vectors for pathogens). The discovery and adaptation of the CRISPR/Cas editing platform co-opted from bacteria has provided a mechanism for a means to alter an entire population. A CRISPR-based gene drive system can allow for the forced propagation of a genetic element that bypasses Mendelian inheritance which can be used to bias sex determination, install exogenous information, or remove endogenous DNA within an entire species. Laboratory studies have demonstrated the potency by which gene drives can operate within insects and other organisms. However, continued research and eventual application face serious opposition regarding issues of policy, biosafety, effectiveness, and reversal. Previous mathematical work has suggested the use of modified gene drive designs that are limited in spread such as daisy chain or underdominance drives. However, no system has yet been proposed that allows for an inducible reversal mechanism without requiring the introduction of additional individuals. Here, we study gene drive effectiveness, fitness, and inducible drive systems that could respond to external stimuli expanding from a previous frequency-based population model. We find that programmed modification during gene drive propagation could serve as a potent safeguard to either slow or completely reverse drive systems and allow for a return to the original wild-type population.

The genetic element s2m has been acquired through horizontal transfer by many distantly related viruses, including the SARS-related coronaviruses. Here we show that s2m is evolutionarily conserved in these viruses. Though several lineages of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) devoid of the element can be found, these variants seem to have been short lived, indicating that they were less evolutionary fit than their s2m-containing counterparts. On a species-level, however, there do not appear to be any losses and this pattern strongly suggests that the s2m element is essential to virus replication in SARS-CoV-2 and related viruses. Further experiments are needed to elucidate the function of s2m.

Female meiotic drive is the phenomenon where a selfish genetic element alters chromosome segregation during female meiosis to segregate to the egg and transmit to the next generation more frequently than Mendelian expectation. While several examples of female meiotic drive have been known for many decades, a molecular understanding of the underlying mechanisms has been elusive. Recent advances in this area in several model species prompts a comparative re-examination of these drive systems. In this review, we compare female meiotic drive of several animal and plant species, highlighting pertinent similarities.

Background: Gene drive technologies (GDTs) bias the inheritance of a genetic element within a population of non-human organisms, promoting its progressive spread across this population. If successful, GDTs may be used to counter intractable problems such as vector-borne diseases. A key issue in the debate on GDTs relates to what governance is appropriate for these technologies. While governance mechanisms for GDTs are to a significant extent proposed and shaped by professional experts, the perspectives of these experts have not been explored in depth.Methods: A total of 33 GDT experts from different professional disciplines were interviewed to identify, better understand, and juxtapose their perspectives on GDT governance. The pseudonymized transcripts were analyzed thematically.Results: Three main themes were identified: (1) engagement of communities, stakeholders, and publics; (2) power dynamics, and (3) decision-making. There was broad consensus amongst respondents that it is important to engage communities, stakeholders, and publics. Nonetheless, respondents had diverging views on the reasons for doing so and the timing and design of engagement. Respondents also outlined complexities and challenges related to engagement. Moreover, they brought up the power dynamics that are present in GDT research. Respondents stressed the importance of preventing the recurrence of historical injustices and reflected on dilemmas regarding whether and to what extent (foreign) researchers can legitimately make demands regarding local governance. Finally, respondents had diverging views on whether decisions about GDTs should be made in the same way as decisions about other environmental interventions, and on the decision-making model that should be used to decide about GDT deployment.Conclusions: The insights obtained in this interview study give rise to recommendations for the design and evaluation of GDT governance. Moreover, these insights point to unresolved normative questions that need to be addressed to move from general commitments to concrete obligations.

Horizontal transfer of genetic elements is a common phenomenon in nature. Both prokaryotes, eukaryotes and viruses have been shown to contain genetic elements acquired through horizontal transfer. Some of these elements may be retained over long periods of time after being integrated into the recipient genome because they offer a selective advantage. The genetic element s2m has been acquired through horizontal transfer by many distantly related viruses, including the SARS-related coronaviruses. Here we show that s2m is evolutionarily conserved within this cluster of viruses and that while several short-lived SARS-CoV-2 lineages devoid of the element have been sequenced, there do not appear to be any species-level losses. This pattern strongly suggests that s2m is essential to virus replication in SARS-CoV-2 and related viruses, and that further experiments are needed to characterize its function.

Significance CRISPR-based gene drive systems—genetic elements which could be engineered to rapidly spread traits through wild populations—could help solve some of humanity’s greatest ecological and public health problems. However, if released, current versions might spread through a nontarget population—possibly across political borders—greatly complicating decision-making. To address this issue, we describe a self-exhausting form of CRISPR-based gene drive called a “daisy-chain drive.” We develop mathematical models which suggest that daisy-chain-drive systems will not spread indefinitely through successive populations, and we report numerous CRISPR targeting sequences which could offer enhanced stability. Particularly if combined with threshold dependence, daisy-drive approaches may become a foundational technique for local ecological engineering., If they are able to spread in wild populations, CRISPR-based gene-drive elements would provide new ways to address ecological problems by altering the traits of wild organisms, but the potential for uncontrolled spread tremendously complicates ethical development and use. Here, we detail a self-exhausting form of CRISPR-based drive system comprising genetic elements arranged in a daisy chain such that each drives the next. “Daisy-drive” systems can locally duplicate any effect achievable by using an equivalent self-propagating drive system, but their capacity to spread is limited by the successive loss of nondriving elements from one end of the chain. Releasing daisy-drive organisms constituting a small fraction of the local wild population can drive a useful genetic element nearly to local fixation for a wide range of fitness parameters without self-propagating spread. We additionally report numerous highly active guide RNA sequences sharing minimal homology that may enable evolutionarily stable daisy drive as well as self-propagating CRISPR-based gene drive. Especially when combined with threshold dependence, daisy drives could simplify decision-making and promote ethical use by enabling local communities to decide whether, when, and how to alter local ecosystems.

Summary Currently, piperazic acid is chemically synthesized using ecologically unfriendly processes. Microbial synthesis from glucose is an attractive alternative to chemical synthesis. In this study, we report the production of L‐piperazic acid via microbial fermentation with the first engineered fungal strain of Aureobasidium melanogenum; this strain was constructed by chassis development, genetic element reconstitution and optimization, synthetic rewiring and constitutive genetic circuit reconstitution, to build a robust L‐piperazic acid synthetic cascade. These genetic modifications enable A. melanogenum to directly convert glucose to L‐piperazic acid without relying on the use of either chemically synthesized precursors or harsh conditions. This bio‐based process overcomes the shortcomings of the conventional synthesis routes. The ultimately engineered strain is a very high‐efficient cell factory that can excrete 1.12 ± 0.05 g l‐1 of L‐piperazic acid after a 120‐h 10.0‐l fed‐batch fermentation; this is the highest titre of L‐piperazic acid reported using a microbial cell factory., L‐piperazic acid via microbial fermentation with the first engineered fungal strain of Aureobasidium melanogenum was achieved. This strain was constructed by chassis development, genetic element reconstitution and optimization, synthetic rewiring, and constitutive genetic circuit reconstitution to build a robust L‐piperazic acid synthetic cascade. The ultimately engineered strain has the highest titer of L‐piperazic acid of 1.12 ± 0.05 g l‐1 ever reported.

Background To provide the consumer with choices of genetically modified organisms (GMO) or non-GMO, official food labeling systems were established in many countries. Because the threshold GMO content values were set to distinguish between “non-GMO” and “GMO” designations, GMO content quantification methods are required for ensuring the appropriateness of labeling. Objective As the number of GMOs is continuously increasing around the world, we set out to develop a low-cost, simple and less biased analytical strategy to cover all necessary detection targets. Methods Digital PCR methods are advantageous compared to the conventional quantitative real-time PCR methods. We developed a digital PCR-based GMO quantification method to evaluate the GMO content in maize grains. To minimize the analytical workload, we adopted multiplex digital PCR targeting the 35S promoter and the nopaline synthase terminator, which are genetic elements commonly introduced in many GMOs. Results Our method is significantly simpler and more precise than the conventional real-time PCR-based methods. Additionally, we found that this method enables quantification of the copy number of GMO DNA without double counting multiple elements (35S promoter and nopaline synthase terminator) tandemly placed in a recombinant DNA construct. Conclusion This is the first report on the development of a genetically modified maize quantification method using a multiplexed genetic element-specific digital PCR method. The tandem effect we report here is quite useful for reducing the bias in the analytical results. Highlights Multiplexed genetic element-specific digital PCR can simplify weight-based GMO quantification and thus should prove useful in light of the continuous increase in the number of GM events.

Budding yeast Saccharomyces cerevisiae has become a model eukaryotic microorganism for targeted genomic manipulation due to its efficient homologous recombination. A few genomic loci, including rDNA, Delta, and Ty1, can be utilized to introduce variable copies of genetic elements into the yeast genome. Here we describe a method that combines in vitro Golden Gate Assembly to assemble one or a complex genetic element in an orderly manner and then integrate it into predetermined multi-copy loci through homologous recombination. Different transformants may contain different copy numbers, which allows the selection of desired levels of target gene expression.

The new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a zoonotic pathogen that has rapidly mutated and become transmissible to humans. There is little existing data on the mutations in SARS-CoV-2 and the impact of these polymorphisms on its transmission and viral load. In this study, the SARS-CoV-2 genomic sequence was analyzed to identify variants within the 3’UTR region of its cis-regulatory RNA elements. A 43-nucleotide genetic element with a highly conserved stem-loop II-like motif (S2M), was discovered. The research revealed 32 G>U and 16 G>U/A mutations located within the S2M sequence in human SARS-CoV-2 models. These polymorphisms appear to make the S2M secondary and tertiary structures in human SARS-CoV-2 models less stable when compared to the S2M structures of bat/pangolin models. This grants the RNA structures more flexibility, which could be one of its escape mechanisms from host defenses or facilitate its entry into host proteins and enzymes. While this S2M sequence may not be omnipresent across all human SARS-CoV-2 models, when present, its sequence is always highly conserved. It may be used as a potential target for the development of vaccines and therapeutic agents.

The term “prion” was originally coined to describe the proteinaceous infectious agents involved in mammalian neurological disorders. More recently, a prion has been defined as a nonchromosomal, protein-based genetic element that is capable of converting the copies of its own benign variant into the prion form, with the new phenotypic effects that can be transmitted through the cytoplasm. Some prions are toxic to the cell, are able to aggregate and/or form amyloid structures, and may be infectious in the wild, but none of those traits are seen as an integral property of all prions. We propose that the definition of prion should be expanded, to include the inducible transmissible entities undergoing autocatalytic conversion and consisting of RNA rather than protein. We show that when seen in this framework, some naturally occurring RNAs, including ribozymes, riboswitches, viroids, viroid-like retroelements, and PIWI-interacting RNAs (piRNAs), possess several of the characteristic properties of prions., A.R.M. is a Program Director at the National Science Foundation (NSF), an agency of the U.S. Government; his work was supported by the NSF’s Independent Research/Development and Long-Term Professional Development Programs, but the statements and opinions expressed herein are made in the personal capacity and do not constitute the endorsement by NSF or the government of the United States. S.F.E. was supported by grants BFU2015-65037-P (Spain Agencia Estatal de Investigación-FEDER) and PROMETEOII/2014/012 (Generalitat Valenciana).

Availability of efficient DNA assembly methods is a basic requirement for synthetic biology. A variety of modular cloning systems have been developed, based on Golden Gate cloning for DNA assembly, to enable users to assemble multigene constructs from libraries of standard parts using a series of successive one-pot assembly reactions. Standard parts contain the DNA sequence coding for a genetic element of interest such as a promoter , coding sequence or terminator . Standard parts for the modular cloning system MoClo must be flanked by two BsaI restriction sites and should not contain internal sequences for two type IIS restriction sites, BsaI and BpiI, and optionally for a third type IIS enzyme, BsmBI. We provide here a detailed protocol for cloning of basic parts. This protocol requires the following steps (1) defining the type of basic part that needs to be cloned, (2) designing primers for amplification, (3) performing PCR amplification, (4) cloning of the fragments using Golden Gate cloning, and finally (5) sequencing of the part. For large basic parts, it is preferable to first clone subparts as intermediate level -1 constructs. These subparts are sequenced individually and are then further assembled to make the final level 0 module.

SPAGE (Self-Propagating Artificial Genetic Element) technologies allow for a proliferation of genetic information on the population level at a higher rate than usual Mendelian inheritance. Currently projected developments of SPAGE mainly aim at a reduction or suppression of animal populations which are considered to be harmful or undesirable (Oye et al. 2014). However, the application of SPAGE is not limited to animals only. In principle, also plant populations can be targeted (National Academies of Sciences 2016). The GeneTip case study on oilseed rape (Brassica napus) is intended to assess, which interactions play a role in a plant-specific context to address relevant ecological interactions that need to be fully explored in order to estimate potential risks.

Gene drive approaches—those which bias inheritance of a genetic element in a population of sexually reproducing organisms—have the potential to provide important public benefits. The spread of selected genetic elements in wild populations of organisms may help address certain challenges, such as transmission of vector-borne human and animal diseases and biodiversity loss due to invasive animals. Adapting various naturally occurring gene drive mechanisms to these aims is a long-standing research area, and recent advances in genetics have made engineering gene drive systems significantly more technically feasible. Gene drive approaches would act through changes in natural environments, thus robust methods to evaluate potential research and use are important.

A systematic review was conducted to determine the distribution and prevalence of antibiotic-resistant bacteria (ARB), antimicrobial-resistant genes (ARGs), and antimicrobial-resistant gene determinants (ARGDs) in clinical, environmental, and farm settings and to identify key knowledge gaps in a bid to contain their spread. Fifty-three articles were included. The prevalence of a wide range of antimicrobial-resistant bacteria and their genes was reviewed. Based on the studies reviewed in this systematic review, mutation was found to be the main genetic element investigated. All settings shared 39 ARGs and ARGDs. Despite the fact that ARGs found in clinical settings are present in the environment, in reviewed articles only 12 were found to be shared between environmental and clinical settings; the inclusion of farm settings with these two settings increased this figure to 32. Data extracted from this review revealed farm settings to be one of the main contributors of antibiotic resistance in healthcare settings. ARB, ARGs, and ARGDs were found to be ubiquitous in all settings examined.

Aim. Goal of the study is characterization and analysis of an occurrence of ICE-emm12 genetic element associated with streptococcal outbreaks, among Vietnamese and Russian GAS strains. Materials and methods. A total of 96 strains isolated in 2007 - 2014 in Moscow, Saint-Petersburg and different provinces of Vietnam were studied. Molecular genetic experiments were done as previously described. Whole genome sequencing was done using MiSeq technology. Results. Complete genome sequencing of Vietnamese strain V31 revealed the presence of 61028 bp fragment homologous to integrative and conjugative element ICE-emm12 containing resistance genes to MLS-antibiotics (ermB) and tetracycline (tetM). This element was discovered in 12 (26,1%, types emm12.0, emm12.22) out of 46 Vietnamese strains, and 2 (4,0%, types emm12.0, emm88.2) out of 50 Russian strains. In 13 out of 14 strains, ICE-emm12 was integrated in RNA-methyltransferase gene, which is possibly the «hot spot» for recombination. In all the strains ICE-emm12 was present in two forms: integrated linearized form and excised circular form with potential to be horizontally transferred. Conclusion. The presence of ICE-emm12 containing antibiotic resistance genes and associated with streptococcal outbreaks in South East Asia, among Russian GAS strains together with the fact of intensive tourism industry indicate the need of molecular epidemiological surveillance for circulation of epidemiologically actual streptococcal clones in Russia.

The import and use of genetically modified organisms (GMOs) is strictly regulated in the European Union. In order to maintain the legislation on GMOs, a genetic element screening is generally applied as a first step to detect authorised as well as unauthorised GMOs. Subsequent identification of GMOs that relate to the detected elements is performed by the application of event-specific detection methods. However, as the diversity of GMOs on the world market is increasing, there is an ongoing need for methods for additional informative screening elements. Genes that are increasingly applied in GMOs are cry3A (including variants mcry3A and eCry3.1Ab) conferring resistance to Bt toxins, and gat, detoxifying glyphosate. Novel TaqMan PCR detection methods for element cry3A and construct gat/T-pinII were developed to support the identification of maize MIR604, 98140, 5307, canola 61061 and 73496, and soybean 356043. Also, other unknown (unauthorised) GMOs containing cry3A and/or gat/T-pinII can potentially be detected. Specificity, efficiency and sensitivity of the methods were evaluated.

Male mate preferences have been demonstrated across a range of species, including the Malaysian stalk-eyed fly,Teleopsis dalmanni. This species is subject to SR, an X-linked male meiotic driver, that causes the dysfunction of Y-sperm and the production all female broods. SR is associated with a low frequency inversion spanning most of the X chromosome that causes reduced organismal fitness. While there has been work considering female avoidance of meiotic drive males, the mating decisions of drive-bearing males have not been considered previously. As drive males are of lower genetic quality they may be less able to bear the cost of choice or may experience weaker selection for its maintenance if they are avoided by females. We investigated preference of drive males using binary choice trials. We confirmed that males prefer to mate with large females (indicative of greater fecundity) but found no evidence that the strength of male mate preference differs between drive and standard males. This suggests that the cost of choice does not restrict male reference among drive males. In a further experiment, we found that large eyespan males showed strong preference whereas small eyespan males showed no preference. This is likely to weaken mate preference in drive males, as on average they have reduced eyespan compared to standard males. In this respect, drive males are subject to and exert weak sexual selection.Lay summaryWe studied male mate preference in stalk-eyed flies. This species suffers from meiotic drive, a selfish genetic element that causes a reduction in sperm production and organismal fitness. We predicted that males with meiotic drive would show weak mate preference. Males preferred to mate with large females, but there was no difference in the strength of preference between drive and non-drive males. Males with larger eyespan showed stronger mate preference. Meiotic drive males usually have reduced eyespan so on average they exert weaker sexual selection on females, but this is mediated by eyespan, not genotypeper se.

Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results., Molecular diagnostic tests can be used to provide rapid identification of staphylococcal species in blood culture bottles to help improve antimicrobial stewardship. However, alterations in the target nucleic acid sequences of the microorganisms or their antimicrobial resistance genes can lead to false-negative results. We determined the whole-genome sequences of 4 blood culture isolates of Staphylococcus aureus and 2 control organisms to understand the genetic basis of genotype-phenotype discrepancies when using the Xpert MRSA/SA BC test (in vitro diagnostic medical device [IVD]). Three methicillin-resistant S. aureus (MRSA) isolates each had a different insertion of a genetic element in the staphylococcal cassette chromosome (SCCmec)-orfX junction region that led to a misclassification as methicillin-susceptible S. aureus (MSSA). One strain contained a deletion in spa, which produced a false S. aureus-negative result. A control strain of S. aureus that harbored an SCCmec element but no mecA (an empty cassette) was correctly called MSSA by the Xpert test. The second control contained an SCCM1 insertion. The updated Xpert MRSA/SA BC test successfully detected both spa and SCCmec variants of MRSA and correctly identified empty-cassette strains of S. aureus as MSSA. Among a sample of 252 MSSA isolates from the United States and Europe, 3.9% contained empty SCCmec cassettes, 1.6% carried SCCM1

SR meiotic drive is a selfish genetic element located on the X chromosome in a number of species that causes dysfunction of Y-bearing sperm. SR is transmitted to up to 100% of offspring, causing extreme sex ratio bias. SR in several species is found in a stable polymorphism at a moderate frequency, suggesting there must be strong frequency-dependent selection resisting its spread. We investigate the effect of SR on female and male egg-to-adult viability in the Malaysian stalk-eyed fly,Teleopsis dalmanni. SR meiotic drive in this species is old, and appears to be broadly stable at a moderate (~20%) frequency. We use large-scale controlled crosses to estimate the strength of selection acting against SR in female and male carriers. We find that SR reduces the egg-to-adult viability of both sexes. In females, homozygous females experience greater reduction in viability (sf= 0.242) and the deleterious effects of SR are additive (ℎ = 0.511). The male deficit in viability (sm= 0.214) is not different from that in homozygous females. The evidence does not support the expectation that deleterious side-effects of SR are recessive or sex-limited. We discuss how these reductions in egg-to-adult survival, as well as other forms of selection acting on SR, act to maintain SR polymorphism in this species.

Gynodioecy is a sexual polymorphism in angiosperms, where hermaphroditic and female individuals coexist. This is often caused by a cytoplasmic genetic element (CGE) that destroys male functions, which is called cytoplasmic male-sterility (CMS). On the other hand, nuclear genes tend to evolve the ability to restore male function. The coevolutionary process of CMS and the restoration has been studied theoretically. Recently, a theoretical study suggested that these coevolutionary dynamics could be influenced by the rate of selfing within populations, although it assumed that the selfing rate of a population was a fixed parameter. Accordingly, we theoretically study the coevolution of three traits in this paper: CMS, nuclear restorer and selfing rate, in which we hypothesize that selfing evolution can suppress CMS evolution under some conditions. The analysis indicates three significant properties of the system; (1) CMS-restorer evolution can result in bistability under a given selfing rate, (2) the coevolution of three traits can realize intermediate levels of selfing, and (3) the evolution of high levels of selfing is conditionally associated with no CMS and/or no restoration, which may support our hypothesis.

The genetic element 'Mona' has been shown previously to be associated with resistance to demethylation inhibitors (DMIs) in Monilinia fructicola. In this study, the promoter activity of the 'Mona' element was demonstrated genetically and the activity was narrowed down to a 20-bp active region through a series of deletions. 'Mona' knockout transformants (ΔMona) were generated from DMI-resistant isolate Bmpc7, and EC50 values and expression of the MfCYP51 gene were found to be reduced in transformants compared with the parental isolate. When the 'Mona' element was inserted into the upstream region of the MfCYP51 gene of the DMI-sensitive isolate HG3, the EC50 values and expression of the MfCYP51 gene increased in the transformants compared with the parental sensitive isolate. These results indicate that the 'Mona' element determines the DMI fungicide resistance through the up-regulation of the expression of the downstream MfCYP51 gene. No fitness penalty was observed in knockout and insertion transformants, i.e. transformants showed similar mycelial growth rate, sporulation and ability to cause lesions on fruit compared with their parental isolates, suggesting that the 'Mona' element does not affect basal life activities.

The current world population contains an ever-increasing increased proportion of the elderly. This is due to global improvements in medical care and access to such care. Thus, a growing incidence of age-related neurodegenerative disorders is to be expected. Increased longevity also allows more time for interaction with adverse environmental factors that have the potential exert a gradual pressure, facilitating the onset of organismic aging. Nearly all neurodegenerative disorders have a relatively minor genetic element and a larger idiopathic component. It is likely that some of the unknown factors promoting neurological disease involve the appearance of some deleterious aspects of senescence, elicited prematurely by low but pervasive levels of toxic materials present in the environment. This review considers the nature of such possible toxicants and how they may hasten neurosenescence. An enhanced rate of emergence of normal age-related changes in the brain can lead to increased incidence of those specific neurological disorders where aging is an essential requirement. In addition, some xenobiotic agents appear to have the capability of engendering specific neurodegenerative disorders and some of these are also considered.

This study used whole-genome sequencing (WGS) and PFGE to analysis KPC-2-producing Klebsiella pneumoniae strains from clinical specimens collected in Brazilian hospitals. The study identifies the emergence of a novel small IncX3 plasmid (pKPB11), 12,757-bp in length, in a high-risk K. pneumoniae ST11/CG258 lineage, a successful clonal group in Brazil, carrying the blaKPC-2 gene on a non-Tn4401 genetic element (NTEKPC-Ic). Comparative analysis of the pKPB11 showed that this plasmid reduced its size, losing part of its conjugation apparatus. The pKPB11 was also compared to another strain sequenced in this study (KPC89) that had the hybrid IncX3-IncU plasmid (pKP89), of approximately 45 kb in length, similarly carrying the blaKPC-2 gene on NTEKPC-Ic. To the best of our knowledge, pKPB11 is the first example of small IncX3 plasmid found in a high-risk KPC-2-producing K. pneumoniae ST11/CG258.

The t haplotype in house mice is a well-known selfish genetic element with detrimental, nonadditive fitness consequences to its carriers: recessive lethal mutations cause t/t homozygotes to perish in utero. Given the severe genetic incompatibility imposed by the t haplotype, we predict females to avoid fertilization by t haplotype incompatible males. Indeed, some of the strongest evidence for compatibility mate choice is related to the t haplotype in house mice. However, all previous evidence for compatibility mate choice in this system is based on olfactory preference. It is so far unknown how general these preferences are and whether they are relevant in an actual mating context. Here, we assess female compatibility mate choice related to t haplotypes in a setting that – for the first time – allowed females to directly interact and mate with males. This approach enabled us to analyse female behaviour during the testing period, and the resulting paternity success and fitness consequences of a given choice. We show that genetic incompatibilities arising from the t haplotype had severe indirect fitness consequences and t females avoided fertilization by t incompatible males. The results are inconclusive whether this avoidance of t fertilization by t females was caused by pre- or post-copulatory processes.

Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans. The element is made up of sup-35, a maternal-effect toxin that kills developing embryos, and pha-1, its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity. Inactive copies of the sup-35/pha-1 element show high sequence divergence from active copies, and phylogenetic reconstruction suggests that they represent ancestral stages in the evolution of the element. Our results suggest that other essential genes identified by genetic screens may turn out to be components of selfish elements.

Background Achalasia is a rare disease with a morbidity of 1 in 100,000, for which the exact mechanism of pathogenesis has not been clarified due to the small total number of patients. We herein report on our experience with two cases of familial achalasia in which the involvement of genetic inheritance was suspected. Case presentation These cases consist of a man in his thirties and his mother in her sixties. The son consulted the Department of Gastrointestinal Medicine at our institute with dysphagia, and an upper gastrointestinal endoscopy revealed a gastric submucosal tumor with a maximal diameter of approximately 50 mm. Achalasia was also strongly suspected due to the enlargement of the esophagus to the maximum transverse diameter of 55 mm by esophagography along with delayed clearance of barium. A detailed interview revealed prolonged mild dysphagia in his mother. Therefore, high-resolution manometry was carried out in both patients. As a result, peristaltic disorder was observed in the esophageal body in both the mother and son, leading to a definitive diagnosis of achalasia. For the son, total gastrectomy including the lower esophagus with Roux-en-Y reconstruction was performed. His postoperative course was uneventful, and the patient was discharged from hospital in remission on the 9th day following surgery and is currently undergoing follow-up as an outpatient. Conclusions We hereby report on a very rare case of familial achalasia that we experienced which may suggest a genetic element in the onset of achalasia, and reviewed the literature.

Use of a pragmatic, affordable and reliable approach for screening and detection of a large number of genetically modified (GM) crops/events is the need of hour. A cost-effective matrix approach to check the GM status of food/feed products and for screening the presence of authorized and unauthorized GM events in India is being reported in the present study. A genetically modified organism (GMO) screening matrix, with the information on 106 genetic element targets for detection of 141 GM events of 21 crops, is being presented. These include commercially cultivated Bt cotton events and other GM events, under field trials during the past six years (2006–2012) in the country. The information on GM events, which were either indigenously developed or imported for research purposes, is also presented in brief. Ten most frequently present targets, viz., [P-35S] [T-nos] [Os-Msca1] [cry1Ab] [cry1Ac] [cry1C] [cry2Ab] [GA20 oxidase1] [nptII] [bar], were identified to screen these events using a GMOseek algorithm. This user-friendly screening tool is flexible for further updates with the new GM events and targets/elements. The data reported here related to the GM crops/events in India and the related GMO matrix are valuable tools to assist in the detection of accidental presence of unauthorized GM events in the food and supply chain globally, as well as in the context of the new labelling requirements for food commodities, as per the amendment to enforce GM food labelling from January 2013 in India. The reported GMO matrix approach would facilitate efficient, rapid and cost-effective preliminary screening by eliminating the need for development of specific testing methodologies for each GM event.

Most current approaches for analyzing metagenomic data rely on comparisons to reference genomes, but the microbial diversity of many environments extends far beyond what is covered by reference databases. De novo segregation of complex metagenomic data into specific biological entities, such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences. We demonstrate the method on data from 396 human gut microbiome samples and identify 7,381 co-abundance gene groups (CAGs), including 741 metagenomic species (MGS). We use these to assemble 238 high-quality microbial genomes and identify affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples.